Single cell type - RNF13 - The Human Protein Atlas

RNF13

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GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	RNF13
Gene descriptionⁱ Full gene name according to HGNC.	Ring finger protein 13
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Enzymes Human disease related genes Metabolic proteins Potential drug targets
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	13

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.	Macrophages - Innate immune response (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Cell type enhanced (Oligodendrocytes, Monocytes)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.36
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enhanced (Oligodendrocyte)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Immune cell enhanced (neutrophil)
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types RNA single cell type specificity: Cell type enhanced (Oligodendrocytes, Monocytes)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Oligodendrocyte)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Immune cell enhanced (neutrophil)
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

RNF13 is part of cluster 58 Macrophages - Innate immune response with confidenceⁱ 1
420 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
MOSPD2	Motile sperm domain containing 2	0.6304	58
GLDN	Gliomedin	0.5943	51
SIRPA	Signal regulatory protein alpha	0.5770	58
PLXDC2	Plexin domain containing 2	0.5341	58
CREB5	CAMP responsive element binding protein 5	0.5224	51
TBC1D12	TBC1 domain family member 12	0.5211	51
HEXA	Hexosaminidase subunit alpha	0.5177	58
MCOLN1	Mucolipin TRP cation channel 1	0.5173	58
RNF130	Ring finger protein 130	0.5094	29
GPNMB	Glycoprotein nmb	0.5072	58
CCL18	C-C motif chemokine ligand 18	0.4999	58
ZFYVE16	Zinc finger FYVE-type containing 16	0.4928	51
FKBP15	FKBP prolyl isomerase family member 15	0.4903	58
MRC1	Mannose receptor C-type 1	0.4886	58
LAMP2	Lysosomal associated membrane protein 2	0.4879	58

IMMUNE CELLS

RNF13 is part of cluster 28 Neutrophils - Unknown function with confidenceⁱ 0.99
118 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
KIAA0513	KIAA0513	0.9762	38
PECAM1	Platelet and endothelial cell adhesion molecule 1	0.9762	37
HCAR3	Hydroxycarboxylic acid receptor 3	0.9762	28
CAPZA2	Capping actin protein of muscle Z-line subunit alpha 2	0.9762	28
MCMBP	Minichromosome maintenance complex binding protein	0.9762	28
MCTP1	Multiple C2 and transmembrane domain containing 1	0.9762	37
TPCN2	Two pore segment channel 2	0.9762	37
NFKBIZ	NFKB inhibitor zeta	0.9762	37
SNX27	Sorting nexin 27	0.9762	40
CALCOCO2	Calcium binding and coiled-coil domain 2	0.9762	28
DGLUCY	D-glutamate cyclase	0.9762	37
TNFSF10	TNF superfamily member 10	0.9762	28
FBXO30	F-box protein 30	0.9762	40
NEDD9	Neural precursor cell expressed, developmentally down-regulated 9	0.9762	28
TMEM33	Transmembrane protein 33	0.9762	38

Adipocytes	96.2 nTPM
Breast	96.9 nTPM
Adipose tissue	95.5 nTPM

Alveolar cells type 1	61.4 nTPM
Lung	61.4 nTPM

Alveolar cells type 2	55.3 nTPM
Lung	55.3 nTPM

Astrocytes	74.6 nTPM
Brain	74.6 nTPM

B-cells	52.3 nTPM
Lymph node	70.2 nTPM
Stomach	65.0 nTPM
Bone marrow	63.4 nTPM
PBMC	58.5 nTPM
Spleen	57.5 nTPM
Skin	55.9 nTPM
Salivary gland	51.2 nTPM
Lung	49.6 nTPM
Liver	48.3 nTPM
Thymus	45.1 nTPM
Adipose tissue	44.0 nTPM
Kidney	41.6 nTPM
Esophagus	29.5 nTPM

Ciliated cells	38.5 nTPM
Lung	43.8 nTPM
Fallopian tube	39.6 nTPM
Bronchus	37.8 nTPM
Endometrium	32.9 nTPM

Club cells	59.9 nTPM
Lung	63.6 nTPM
Bronchus	61.7 nTPM
Prostate	54.5 nTPM

Dendritic cells	85.7 nTPM
PBMC	93.5 nTPM
Adipose tissue	77.9 nTPM

Endothelial cells	66.7 nTPM
Skin	116.3 nTPM
Breast	100.2 nTPM
Skeletal muscle	95.2 nTPM
Esophagus	76.5 nTPM
Prostate	70.7 nTPM
Heart muscle	70.3 nTPM
Salivary gland	70.1 nTPM
Thymus	65.9 nTPM
Lung	65.0 nTPM
Vascular	65.0 nTPM
Testis	64.1 nTPM
Tongue	59.8 nTPM
Fallopian tube	59.5 nTPM
Liver	50.4 nTPM
Ovary	48.2 nTPM
Placenta	45.4 nTPM
Endometrium	39.7 nTPM
Pancreas	38.8 nTPM

Enteroendocrine cells	24.6 nTPM
Colon	39.9 nTPM
Small intestine	17.2 nTPM
Rectum	16.8 nTPM

Fibroblasts	82.4 nTPM
Adipose tissue	130.1 nTPM
Skeletal muscle	125.3 nTPM
Skin	109.1 nTPM
Esophagus	104.6 nTPM
Liver	102.0 nTPM
Stomach	93.7 nTPM
Breast	84.4 nTPM
Heart muscle	82.5 nTPM
Salivary gland	78.5 nTPM
Thymus	68.9 nTPM
Prostate	68.0 nTPM
Vascular	67.6 nTPM
Placenta	66.3 nTPM
Fallopian tube	61.8 nTPM
Lung	48.2 nTPM
Pancreas	27.1 nTPM

Granulocytes	47.7 nTPM
Lung	64.5 nTPM
Fallopian tube	54.2 nTPM
Tongue	24.3 nTPM

Intestinal goblet cells	30.2 nTPM
Small intestine	32.8 nTPM
Colon	32.2 nTPM
Rectum	25.7 nTPM

Lymphatic endothelial cells	46.0 nTPM
Fallopian tube	70.2 nTPM
Ovary	21.8 nTPM

Macrophages	173.2 nTPM
Lung	282.7 nTPM
Testis	277.1 nTPM
Spleen	213.5 nTPM
Stomach	208.3 nTPM
Adipose tissue	203.4 nTPM
Esophagus	179.8 nTPM
Skin	173.8 nTPM
Prostate	170.9 nTPM
Vascular	168.4 nTPM
Skeletal muscle	167.2 nTPM
Fallopian tube	165.9 nTPM
Bone marrow	165.2 nTPM
Kidney	159.3 nTPM
Salivary gland	156.7 nTPM
Pancreas	150.1 nTPM
Thymus	142.1 nTPM
Breast	132.7 nTPM
Tongue	115.3 nTPM
Endometrium	58.4 nTPM

Basal keratinocytes	57.7 nTPM
Skin	65.4 nTPM
Tongue	50.0 nTPM

Basal prostatic cells	50.7 nTPM
Prostate	50.7 nTPM

Basal respiratory cells	79.1 nTPM
Bronchus	79.1 nTPM

Basal squamous epithelial cells	62.0 nTPM
Esophagus	62.0 nTPM

Paneth cells	41.2 nTPM
Small intestine	51.8 nTPM
Colon	39.8 nTPM
Rectum	32.1 nTPM

Plasma cells	58.7 nTPM
Esophagus	83.2 nTPM
Fallopian tube	77.8 nTPM
Stomach	69.1 nTPM
Spleen	56.5 nTPM
Salivary gland	53.7 nTPM
Bone marrow	51.3 nTPM
Thymus	41.5 nTPM
Liver	36.6 nTPM

Schwann cells	83.2 nTPM
Vascular	128.5 nTPM
Esophagus	71.9 nTPM
Adipose tissue	49.2 nTPM

Serous glandular cells	84.2 nTPM
Salivary gland	128.7 nTPM
Tongue	39.8 nTPM

Smooth muscle cells	53.8 nTPM
Liver	73.4 nTPM
Placenta	70.9 nTPM
Skeletal muscle	65.1 nTPM
Salivary gland	63.6 nTPM
Tongue	59.6 nTPM
Adipose tissue	59.0 nTPM
Esophagus	57.7 nTPM
Skin	55.0 nTPM
Fallopian tube	53.3 nTPM
Lung	51.7 nTPM
Vascular	48.8 nTPM
Prostate	47.4 nTPM
Breast	47.4 nTPM
Ovary	44.8 nTPM
Thymus	38.8 nTPM
Endometrium	24.7 nTPM

Suprabasal keratinocytes	64.4 nTPM
Skin	69.9 nTPM
Tongue	58.9 nTPM

T-cells	45.3 nTPM
Spleen	57.3 nTPM
Lymph node	56.6 nTPM
Kidney	55.9 nTPM
Skin	55.0 nTPM
Esophagus	51.1 nTPM
Bone marrow	50.9 nTPM
Breast	49.7 nTPM
Stomach	48.9 nTPM
Prostate	45.4 nTPM
Colon	44.8 nTPM
Lung	44.3 nTPM
Thymus	44.0 nTPM
Liver	43.8 nTPM
Salivary gland	42.3 nTPM
Skeletal muscle	40.1 nTPM
PBMC	39.9 nTPM
Tongue	39.7 nTPM
Fallopian tube	39.6 nTPM
Vascular	38.6 nTPM
Adipose tissue	36.7 nTPM
Endometrium	26.9 nTPM

Undifferentiated cells	33.3 nTPM
Colon	35.3 nTPM
Small intestine	34.6 nTPM
Rectum	30.0 nTPM

Amygdala excitatory	136.4 nTPM
Basal ganglia	163.3 nTPM
Amygdala	144.6 nTPM
Cerebral cortex	132.9 nTPM
Hypothalamus	131.7 nTPM
Thalamus	126.6 nTPM
Hippocampus	119.1 nTPM

Astrocyte	168.4 nTPM
Hypothalamus	229.1 nTPM
Amygdala	210.9 nTPM
Basal ganglia	170.2 nTPM
Cerebral cortex	167.2 nTPM
Spinal cord	165.7 nTPM
Hippocampus	162.2 nTPM
Pons	156.1 nTPM
Medulla oblongata	154.8 nTPM
Midbrain	150.6 nTPM
Thalamus	149.2 nTPM
Cerebellum	136.6 nTPM

Bergmann glia	224.8 nTPM
Medulla oblongata	234.4 nTPM
Pons	223.0 nTPM
Cerebellum	217.0 nTPM

Central nervous system macrophage	446.0 nTPM
Amygdala	550.7 nTPM
Hypothalamus	489.7 nTPM
Basal ganglia	482.6 nTPM
Spinal cord	459.0 nTPM
Pons	440.0 nTPM
Midbrain	432.5 nTPM
Thalamus	431.7 nTPM
Medulla oblongata	412.0 nTPM
Hippocampus	408.5 nTPM
Cerebellum	405.7 nTPM
Cerebral cortex	393.3 nTPM

Cerebellar inhibitory	138.4 nTPM
Pons	154.9 nTPM
Medulla oblongata	149.1 nTPM
Midbrain	136.6 nTPM
Cerebellum	130.4 nTPM
Spinal cord	121.0 nTPM

Cge interneuron	119.7 nTPM
Thalamus	132.7 nTPM
Amygdala	129.5 nTPM
Midbrain	124.7 nTPM
Basal ganglia	117.4 nTPM
Cerebral cortex	111.5 nTPM
Hypothalamus	111.2 nTPM
Hippocampus	111.1 nTPM

Choroid plexus epithelial cell	253.4 nTPM
Basal ganglia	276.9 nTPM
Thalamus	260.3 nTPM
Hippocampus	246.8 nTPM
Medulla oblongata	229.6 nTPM

Committed oligodendrocyte precursor	350.1 nTPM
Hypothalamus	441.8 nTPM
Thalamus	402.3 nTPM
Midbrain	379.7 nTPM
Amygdala	358.1 nTPM
Cerebellum	356.7 nTPM
Spinal cord	342.2 nTPM
Basal ganglia	334.0 nTPM
Cerebral cortex	333.8 nTPM
Pons	332.9 nTPM
Hippocampus	302.9 nTPM
Medulla oblongata	267.2 nTPM

Deep-layer corticothalamic and 6b	191.2 nTPM
Midbrain	208.6 nTPM
Amygdala	205.4 nTPM
Cerebral cortex	191.6 nTPM
Hippocampus	189.2 nTPM
Basal ganglia	184.9 nTPM
Hypothalamus	167.5 nTPM

Deep-layer intratelencephalic	179.1 nTPM
Hippocampus	189.8 nTPM
Basal ganglia	183.1 nTPM
Amygdala	178.1 nTPM
Cerebral cortex	176.5 nTPM
Hypothalamus	168.3 nTPM

Deep-layer near-projecting	144.8 nTPM
Basal ganglia	148.6 nTPM
Amygdala	147.2 nTPM
Hippocampus	146.4 nTPM
Cerebral cortex	144.6 nTPM
Hypothalamus	137.0 nTPM

Eccentric medium spiny neuron	140.8 nTPM
Amygdala	148.9 nTPM
Thalamus	146.6 nTPM
Basal ganglia	142.3 nTPM
Hypothalamus	142.3 nTPM
Cerebral cortex	138.6 nTPM
Hippocampus	126.0 nTPM